Is Your Water Safe to Drink? Ask the Microbes


Two hands holding water.While invisible to the naked eye, seemingly clear water can be full of microorganisms. Some microbes, like Escherichia coli (E. coli), can cause adverse health effects. But others, like Dokdonella kunshanensis, could actually be used to purify wastewater. Thus, the presence of microbes in water poses the question: are they friends or foes?

A Call for Testing

Every year, there are millions of reported cases of waterborne diseases, including typhoid fever and cholera. There are 11 million cases of typhoid fever globally, resulting in 129,000 deaths. Additionally, there are 3 million cases of cholera globally and 95,000 related deaths. According to the Lancet 2015 Global Burden of Disease study, more than 6.5 million cases of acute diarrhea occur globally each day. These cases are primarily the result of waterborne diseases that inconspicuously lurk beneath the water’s surface, like rotavirus (caused by rotavirus gastroenteritis), cholera (caused by Vibrio cholerae) and dysentery (caused by Shigella), and are often contracted through drinking water. According to the World Health Organization (WHO), more than 2 billion people do not have access to safe drinking water.

“You don't see the microorganisms that cause the disease when they could be present in the water,” said Dr. Kehinde Eniola, dean of the College of Postgraduate Studies at Joseph Ayo Babalola University in Osun State, Nigeria. This is why testing for pathogens in drinking water is incredibly important. Even the clearest water could have contaminants from fecal matter. Testing drinking water can identify both the presence of harmful microbes and the level of risk associated with the water source, which could help a community mitigate the spread of waterborne diseases. “It’s like if someone says, ‘I don't have COVID-19,’ you would say, ‘I'm going to test you first,’” Eniola continued. “So only a negative PCR test will tell you if you are free of COVID-19.”

Evidence-based Microbiology at the Community Level

Water-testing kits can serve as educational tools that demonstrate best practices for identifying safe drinking water. In Lower Nyakach, Kisumu County, Kenya, its population of 70,000 has little to no access to safe drinking water. “They've got a shallow well; they are getting water from their river,” said Dr. Robert Metcalf, a professor emeritus of biological sciences at California State University, Sacramento and co-founder and president of the International Water and Health Alliances. “And the most important public health piece of information you’ve got to have is whether the water that you’re drinking is safe to drink or not.”

Metcalf has worked with the Friends of the Old (FOTO) leadership team since before the project’s inception. FOTO aims to eliminate cases of waterborne diseases completely in Lower Nyakach. As a result of community-based education, community members in Lower Nyakach are more aware of water quality and disease-detection practices. “Instead of trying to get 5 more vaccines for pathogens found in drinking water that are going to be hard to distribute and pay for, let's empower community-based organizations, like FOTO,” Metcalf said. He explained that between the 2 types of prevention strategies—removing the threat (e.g., water sanitation) and conditioning one’s immune system to recognize pathogens upon exposure (e.g., vaccines)—the former is more cost-effective and practical at the community level. “Let’s ensure [community-based organizations] have enough funds to get chlorine, distribute it to people and provide education about how to use it,” he said.





According to Dinah Chienjo, the project director of FOTO, 95% of community members in Lower Nyakach are treating their drinking water by boiling the water or sterilizing it with chlorine. She explained that this is a result of water-testing and purification education that uses the local language, which community members easily understand, and is delivered by local women who they know well and can easily identify with. “There are many communities that drink water that isn’t safe,” Chienjo said. “They need to know that they can do something about it to make it safe—so they can change their health, so they can be healthier, and their children can be healthier.”

Chienjo added that FOTO also educates children in schools, demonstrating how to test and treat their water, practices that can be easily replicated in many parts of the world to eliminate waterborne diseases. While neighboring districts saw a high number of cases of cholera between February and May 2015, Lower Nyakach did not see any cases of cholera and recorded a decrease in cases of diarrhea. Between 2012 and 2016, 4,000 families in Lower Nyakach were provided with solar Cookits, which use solar energy to heat and pasteurize water. Since 2012, the community also has been provided with chlorine for water treatment every month, including 62 primary and 17 secondary schools in the project area.

Five water tests in progress."Numerous programs that focus on water purification require large, expensive pieces of equipment that a community might not have access to, even in a large city," explained Dr. Musau WaKabongo, the founder and CEO of Dr. Musau WaKabongo Science Education, Inc. and co-founder of the African Initiative Group. “There are many programs and projects focused on water purification. But are they practical at the village level?” For WaKabongo, education is key. Equipment cannot simply be dropped off at a location without explanation or demonstrated results. “To teach people water treatment,” she said, “you really need to go to them. You need to talk to them in their language.”

WaKabongo said building relationships and credibility in a community is integral to implementing and sustaining water-testing and purification practices. “The only way to win the community’s trust is whatever you are doing must be done in their presence, they must be witnesses,” she said. “The moment you take anything away from their presence, they doubt you. And that's where portable microbiology laboratories (PMLs) seem to give an edge, because now you do it yourself.”

Last year, in the Democratic Republic of Congo, WaKabongo helped train adults and children on how to test water safety using PMLs in the village of Mpoyi and Tshibombo, a city of displaced people in the Kasai-Oriental Province. The hope is that providing testing materials will enable the community to have safe water and lower the risk of disease.

"You Can Be a Water Microbiologist"

Microscopic view of E. coli bacteria.Some standard water-testing practices are not affordable or accessible in under-resourced communities. However, PMLs, which require less equipment and cost around $1 per test, can check for the presence of E. coli, using just 10 milliliter of water. Many waterborne diseases, like cholera and typhoid, are often associated with fecal contamination. When German physician and microbiologist Robert Koch’s methods in the 1880s led to the discovery that bacteria from feces cause diseases, testing for all diseases associated with fecal contamination was understood to be impractical, so scientists quested after a microbe that would survive as long as most types of bacterial pathogens: E. coli. Additionally, the presence or absence of E. coli is typically used as an indicator of water safety because it is found in a large number of fecal samples and bacterial colonies are easy to count, if sampled.

PMLs include a Colilert 10 milliliter presence/absence test, an E. coli count Petrifilm, a plastic spreader, a sterile collecting bag, a sterile plastic pipette and a long-wavelength UV light. Water samples are collected and first tested for the presence of E. coli. Then, using the Petrifilm—a quantitative test to estimate the number of E. coli present per milliliter—bacteria from the sample is grown to help assess the risk level of the water. “Much of what we do in microbiology labs is a little mysterious,” said Metcalf. “But with the right tools, you can be a water microbiologist.”

Portable microbiology laboratory materials for water testing.UNICEF recommends testing 100 milliliters (a more expensive option at about $4 per test) of water and utilizing membrane filtration, which can cost upwards of $2,000, to detect the presence of E. coli. But Metcalf says collecting such a large water sample is not always necessary. If there’s no presence of E. coli in a 10 milliliter sample, he says, the risk of disease is low. “High” risk is defined as 1-10 E. coli per milliliter, and “very high” risk is defined as more than 10 E. coli per milliliter, according to the WHO Guidelines for Drinking Water Quality.

How to Conduct a Colilert Test

Graphic showing collection of water.
Graphic showing someone adding the water sample using a pipette
Graphic showing putting a test tube in a shirt pocket.
Comparing two sets of samples.
  1. Collect a water sample of about 100 milliliters from the source.
  2. Pipette 10 milliliters of the sample into the presence/absence test.
  3. Incubate the sample for 12-18 hours. The average body temperature of about 37 degrees Celsius happens to provide an ideal environment for bacterial cell growth, so sealed test tubes can even be carried in one’s pocket to incubate the sample.
  4. If the sample turns yellow, determine whether E. coli is present by using the UV light. If the sample produces fluorescence, E. coli is present in the sample. Colilert tests rely on 2 food sources to grow E. coli and environmental bacteria: Ortho-Nitrophenyl-β-galactoside (ONPG) and 4-methylumbelliferyl-β-D-glucuronide (MUG). The latter is only used by E. coli, and when the bacteria metabolizes MUG, it produces fluorescence.

How to Use a Petrifilm

Graphic showing how the test works.
Use a spreader to distribute the water sample evenly.
Graphic showing sample being put in shirt pocket.
Inspect and count the bacteria colonies on the Petrifilm.
  1. Pipette 1 milliliter of the water sample onto the Petrifilm. Unlike other tests, utilizing a Petrifilm forgoes the need for autoclaves, petri dishes and agar media. The Petrifilm test uses 2 substrates—lactose and 5-bromo-4-chloro-3-indoxyl-β-D-glucuronide (BCIG)—which are metabolized by E. coli.
  2. Place the plastic spreader on top of the Petrifilm to distribute the water sample evenly. Let the sample sit for 1 minute to allow the gelling agent to bind to the nutrients on the film.
  3. Incubate the sample for 8-10 hours at body temperature (37 degrees Celsius). This allows for the sample to grow to about 1 million cells, making the bacteria colonies visible on the Petrifilm.
  4. Count the bacteria colonies on the Petrifilm. If no bacteria are visible on the Petrifilm, the risk level is classified as “low” or “moderate.” If 1-10 E. coli are present, the risk is “high,” and finding more than 10 E. coli is considered “very high” risk, according to the WHO Guidelines for Drinking Water Quality.


Petrifilm with bacteria.

Disinfect Before You Drink

You’ve identified bacteria in your water source, which means it’s not safe to drink. Now what? Metcalf recommends 2 options: Boil the water, or use chlorine.

A Water Pasteurization Indicator (WAPI) takes the temperature of a water sample.If you heat water to 65 degrees Celsius, pathogenic organisms, including Giardia, Entamoeba, Cryptosporidium, E. coli, Shigella, cholera, typhoid, rotaviruses, polioviruses and hepatitis A viruses, will be killed. In place of a thermometer, a device the size of your thumb called a Water Pasteurization Indicator (WAPI) can tell you when the water temperature arrives at 65 degrees Celsius. The WAPI consists of a sealed tube filled with wax, which is attached to a fishline with a metal washer at the end that can be dipped into the boiling water. As the water’s temperature increases, the wax inside the WAPI will start to move toward the bottom of the interior.

If you opt to use chlorine, about 20 liters of water can be purified using a bottle cap’s worth of the chemical element. After adding the chlorine and waiting about 30-45 minutes, the water is safe to drink. However, after 4 days, chlorine weakens as a purifying agent, and the water should be repurposed for something other than drinking.

Author: Leah Potter

Leah Potter
Leah Potter joined ASM in 2022 as the communications specialist.

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